@Book{xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.org/knitr/},
}

@article{macintyre2018copy,
  title={Copy number signatures and mutational processes in ovarian carcinoma},
  author={Macintyre, Geoff and Goranova, Teodora E and De Silva, Dilrini and Ennis, Darren and Piskorz, Anna M and Eldridge, Matthew and Sie, Daoud and Lewsley, Liz-Anne and Hanif, Aishah and Wilson, Cheryl and others},
  journal={Nature genetics},
  volume={50},
  number={9},
  pages={1262--1270},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{alexandrov2020repertoire,
  title={The repertoire of mutational signatures in human cancer},
  author={Alexandrov, Ludmil B and Kim, Jaegil and Haradhvala, Nicholas J and Huang, Mi Ni and Ng, Alvin Wei Tian and Wu, Yang and Boot, Arnoud and Covington, Kyle R and Gordenin, Dmitry A and Bergstrom, Erik N and others},
  journal={Nature},
  volume={578},
  number={7793},
  pages={94--101},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{mayakonda2018maftools,
  title={Maftools: efficient and comprehensive analysis of somatic variants in cancer},
  author={Mayakonda, Anand and Lin, De-Chen and Assenov, Yassen and Plass, Christoph and Koeffler, H Phillip},
  journal={Genome research},
  volume={28},
  number={11},
  pages={1747--1756},
  year={2018},
  publisher={Cold Spring Harbor Lab}
}

@article{gaujoux2010flexible,
  title={A flexible R package for nonnegative matrix factorization},
  author={Gaujoux, Renaud and Seoighe, Cathal},
  journal={BMC bioinformatics},
  volume={11},
  number={1},
  pages={367},
  year={2010},
  publisher={Springer}
}

@article{tan2012automatic,
  title={Automatic relevance determination in nonnegative matrix factorization with the/spl beta/-divergence},
  author={Tan, Vincent YF and F{\'e}votte, C{\'e}dric},
  journal={IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume={35},
  number={7},
  pages={1592--1605},
  year={2012},
  publisher={IEEE}
}

@article{kim2016somatic,
  title={Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors},
  author={Kim, Jaegil and Mouw, Kent W and Polak, Paz and Braunstein, Lior Z and Kamburov, Atanas and Tiao, Grace and Kwiatkowski, David J and Rosenberg, Jonathan E and Van Allen, Eliezer M and D D'Andrea, Alan and others},
  journal={Nature genetics},
  volume={48},
  number={6},
  pages={600},
  year={2016},
  publisher={Nature Publishing Group}
}s
@Book{xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.org/knitr/},
}


@article {WangSX2020,
	author = {Wang, Shixiang and Li, Huimin and Song, Minfang and He, Zaoke and Wu, Tao and Wang, Xuan and Tao, Ziyu and Wu, Kai and Liu, Xue-Song},
	title = {Copy number signature analyses in prostate cancer reveal distinct etiologies and clinical outcomes},
	elocation-id = {2020.04.27.20082404},
	year = {2020},
	doi = {10.1101/2020.04.27.20082404},
	publisher = {Cold Spring Harbor Laboratory Press},
	abstract = {Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures of single base substitution (SBS) have been extensively studied in different types of cancer, however, signatures of cancer genome copy number alteration (CNA) are still elusive in most cancer types, especially in prostate cancer (PC), which is particularly driven by complex genome alterations. Here, a user-friendly open source bioinformatics tool "sigminer" has been constructed for copy number signature extraction, analysis and visualization. Five copy number signatures are identified from human PC genome with this tool. The underlying driving forces for each signature have been illustrated. Sample clustering based on copy number signature exposure revealed considerable heterogeneity of PC, and copy number signatures show improved PC clinical outcome association when compared with SBS signatures. Copy number signature analyses provide distinct insight into the etiology of PC, and potential biomarkers for PC stratification and prognosis.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThis work was supported in part by The National Natural Science Foundation of China (31771373), and startup funding from ShanghaiTech University.Author DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll code required to reproduce the analysis outlined in this manuscript are freely available at https://github.com/ShixiangWang/prad_signature. Analyses can be read online at https://shixiangwang.github.io/prad_signature/.},
	URL = {https://www.medrxiv.org/content/early/2020/04/29/2020.04.27.20082404},
	eprint = {https://www.medrxiv.org/content/early/2020/04/29/2020.04.27.20082404.full.pdf},
	journal = {medRxiv}
}



@article{hanahanHallmarksCancerNext2011,
  title = {Hallmarks of {{Cancer}}: {{The Next Generation}}},
  author = {Hanahan, Douglas},
  date = {2011-03-04},
  journaltitle = {Cell},
  shortjournal = {Cell},
  pages = {29},
  doi = {10.1016/j.cell.2011.02.013},
  file = {/Users/wsx/Nutstore Files/zotero-tablet/hanahan_hallmarks_of_cancer.pdf},
  langid = {english}
}


@article{alexandrov2013signatures,
  title={Signatures of mutational processes in human cancer},
  author={Alexandrov, Ludmil B and Nik-Zainal, Serena and Wedge, David C and Aparicio, Samuel AJR and Behjati, Sam and Biankin, Andrew V and Bignell, Graham R and Bolli, Niccolo and Borg, Ake and B{\o}rresen-Dale, Anne-Lise and others},
  journal={Nature},
  volume={500},
  number={7463},
  pages={415--421},
  year={2013},
  publisher={Nature Publishing Group}
}


@article{wang2021copy,
  title={Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes},
  author={Wang, Shixiang and Li, Huimin and Song, Minfang and Tao, Ziyu and Wu, Tao and He, Zaoke and Zhao, Xiangyu and Wu, Kai and Liu, Xue-Song},
  journal={PLoS genetics},
  volume={17},
  number={5},
  pages={e1009557},
  year={2021},
  publisher={Public Library of Science San Francisco, CA USA}
}


@article{nik2016landscape,
  title={Landscape of somatic mutations in 560 breast cancer whole-genome sequences},
  author={Nik-Zainal, Serena and Davies, Helen and Staaf, Johan and Ramakrishna, Manasa and Glodzik, Dominik and Zou, Xueqing and Martincorena, Inigo and Alexandrov, Ludmil B and Martin, Sancha and Wedge, David C and others},
  journal={Nature},
  volume={534},
  number={7605},
  pages={47--54},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{steele2021signatures,
  title={Signatures of copy number alterations in human cancer},
  author={Steele, Christopher D and Abbasi, Ammal and Islam, Ashiqul SM and Khandekar, Azhar and Haase, Kerstin and Hames, Shadi and Tarabichi, Maxime and Lesluyes, Tom and Flanagan, Adrienne M and Mertens, Fredrik and others},
  journal={bioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}

@article{hillman2018genomic,
  title={Genomic rearrangement signatures and clinical outcomes in high-grade serous ovarian cancer},
  author={Hillman, R Tyler and Chisholm, Gary B and Lu, Karen H and Futreal, P Andrew},
  journal={JNCI: Journal of the National Cancer Institute},
  volume={110},
  number={3},
  pages={265--272},
  year={2018},
  publisher={Oxford University Press}
}

@article{degasperi2020practical,
  title={A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies},
  author={Degasperi, Andrea and Amarante, Tauanne Dias and Czarnecki, Jan and Shooter, Scott and Zou, Xueqing and Glodzik, Dominik and Morganella, Sandro and Nanda, Arjun S and Badja, Cherif and Koh, Gene and others},
  journal={Nature cancer},
  volume={1},
  number={2},
  pages={249--263},
  year={2020},
  publisher={Nature Publishing Group}
}
